Modified-base probability plot using computeMAtrix and HeatMap

[santoshbiowarrior333]

Hi,

I am trying to plot the individual base modifications in a modkit processed mod-bam file.

My data very much looks like this; chr1 596159 596159 0.024414063 chr1 596189 596189 0.016601563 chr1 596190 596190 0.016601563 chr1 596202 596202 0.020507813 chr1 596204 596204 0.020507813 chr1 596205 596205 0.018554688 chr1 596209 596209 0.018554688

Chromosomes, positions that are modified, and %of modification.

This is a region that i have called modified bases for, But i have other bed file that i am using as reference-points in that range.

Now i am getting the blank lines in the plot:

Code used: computeMatrix reference-point --regionsFileName ../../subset_brdU/AsiSI_T2T.bed --scoreFileName output.bw --upstream 2000 --downstream 2000 --missingDataAsZero --outFileName matrix.gz Skipping AsiSI_cutting_sites_r2840, due to being absent in the computeMatrix output. Skipping AsiSI_cutting_sites_r2841, due to being absent in the computeMatrix output. Skipping AsiSI_cutting_sites_r2842, due to being absent in the computeMatrix output. Skipping AsiSI_cutting_sites_r2843, due to being absent in the computeMatrix output. .......

Also there are many Nan's But in my data its evident in the bedgraph that there are many points above 0.7 that is 70%mod.

Heat Map obtained:

I will be very grateful if any help could be provided.